typo

.gitattributes

@@ -2,4 +2,5 @@
 **/.git* annex.largefiles=nothing
 CHANGELOG.md annex.largefiles=nothing
 README.md annex.largefiles=nothing
-.github annex.largefiles=nothing
+.github/**/*.yml annex.largefiles=nothing
+*.def annex.largefiles=nothing

.github/workflows/docker.yml

@@ -1,28 +1 @@
----
-name: docker build
-
-on:
-    push:
-        branches: [master]
-    pull_request:
-
-concurrency:
-    group: ${{ github.workflow }}-${{ github.ref }}
-    cancel-in-progress: true
-
-jobs:
-
-    build:
-        strategy:
-            matrix:
-                image: [dockerfile_MCR, Dockerfile]
-            fail-fast: false
-        runs-on: ubuntu-latest
-        steps:
-        -   uses: actions/checkout@v4
-            with:
-                fetch-depth: 0
-        -   name: Build the Docker image
-            run: |
-                docker build . --file ${{ matrix.image }} --tag cat12
-                docker images
+/annex/objects/MD5E-s908--d79893dc28bfcb54aa92dd21c567641a.yml

.gitignore

@@ -1 +1,4 @@
 .simg
+
+tests/data/raw
+tests/data/MoAEpilot

Dockerfile_1

@@ -0,0 +1,84 @@
+# Generated by Neurodocker and Reproenv.
+
+FROM ubuntu:22.04
+ENV LANG="en_US.UTF-8" \
+    LC_ALL="en_US.UTF-8" \
+    ND_ENTRYPOINT="/neurodocker/startup.sh"
+RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
+    && apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           apt-utils \
+           bzip2 \
+           ca-certificates \
+           curl \
+           locales \
+           unzip \
+    && rm -rf /var/lib/apt/lists/* \
+    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
+    && dpkg-reconfigure --frontend=noninteractive locales \
+    && update-locale LANG="en_US.UTF-8" \
+    && chmod 777 /opt && chmod a+s /opt \
+    && mkdir -p /neurodocker \
+    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
+         echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
+    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
+    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
+    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
+    fi \
+    && chmod -R 777 /neurodocker && chmod a+s /neurodocker
+ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/MCR-2017b/v93/runtime/glnxa64:/opt/MCR-2017b/v93/bin/glnxa64:/opt/MCR-2017b/v93/sys/os/glnxa64:/opt/MCR-2017b/v93/extern/bin/glnxa64" \
+    MATLABCMD="/opt/MCR-2017b/v93/toolbox/matlab" \
+    XAPPLRESDIR="/opt//opt/MCR-2017b/v93/x11/app-defaults" \
+    MCRROOT="/opt/MCR-2017b/v93"
+RUN export TMPDIR="$(mktemp -d)" \
+    && apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           bc \
+           curl \
+           dbus-x11 \
+           libncurses5 \
+           libxext6 \
+           libxmu6 \
+           libxpm-dev \
+           libxt6 \
+           openjdk-8-jre \
+           unzip \
+    && rm -rf /var/lib/apt/lists/* \
+    && echo "Downloading MATLAB Compiler Runtime ..." \
+    && curl  -o "$TMPDIR/mcr.zip" https://ssd.mathworks.com/supportfiles/downloads/R2017b/deployment_files/R2017b/installers/glnxa64/MCR_R2017b_glnxa64_installer.zip \
+    && unzip -q "$TMPDIR/mcr.zip" -d "$TMPDIR/mcrtmp" \
+    && "$TMPDIR/mcrtmp/install" -destinationFolder /opt/MCR-2017b -mode silent -agreeToLicense yes \
+    && rm -rf "$TMPDIR" \
+    && unset TMPDIR
+ENV CAT_VERSION=".8.1_r2042_R2017b"
+ENV FORCE_SPMMCR="1" \
+    SPM_HTML_BROWSER="0" \
+    MCR_INHIBIT_CTF_LOCK="1" \
+    SPMROOT="/opt/CAT12${CAT_VERSION}" \
+    PATH="/opt/CAT12${CAT_VERSION}:$PATH" \
+    STANDALONE="/opt/CAT12${CAT_VERSION}/standalone"
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           ca-certificates \
+           curl \
+           unzip \
+    && rm -rf /var/lib/apt/lists/* \
+    # Install cat12
+    && echo "Downloading standalone CAT12 ..." \
+    && curl -fL -o /tmp/cat12.zip http://www.neuro.uni-jena.de/cat12/CAT12${CAT_VERSION}_MCR_Linux.zip \
+    && unzip -q /tmp/cat12.zip -d /tmp \
+    && rm -rf /tmp/cat12.zip \
+    && mkdir -p /opt/CAT12${CAT_VERSION} \
+    && mv /tmp/*${CAT_VERSION}*/* /opt/CAT12${CAT_VERSION}/ \
+    && chmod -R 777 /opt/CAT12${CAT_VERSION} \
+    # Test
+    && /opt/CAT12${CAT_VERSION}/spm12 function exit
+
+# transfer code and set permission
+RUN mkdir -p /code
+COPY ./code /code
+RUN ls /code && find /code -type f -print0 | xargs -0 chmod +r
+
+WORKDIR ${STANDALONE}
+
+ENTRYPOINT ["/code/main"]

Singularity.def

@@ -0,0 +1 @@
+/annex/objects/MD5E-s6255--ac5590f5bdfc1188a9692c0eea2b36e5.def

Singularity_MCR.def

@@ -0,0 +1 @@
+/annex/objects/MD5E-s16982--97fcbeaf066ad61012381ffe82b98551.def

code/main

@@ -1,18 +1,15 @@
 #!/bin/bash
 
-# Help
+# Copy or view batch files
 
+# Help
 if [ "$#" = 0 ]
 then
     echo "ERROR: No arguments passed."
-    cat /.singularity.d/runscript.help
+    exec ${STANDALONE}/cat_standalone.sh
     exit 1
 fi
 
-# Copy or view batch files
-
-STANDALONE="/opt/spm12/toolbox/cat12/standalone"
-
 if [ "$1" = "copy" ]
 then
     if [ "$2" = "all" ]
@@ -37,13 +34,12 @@ then
 	cat ${STANDALONE}/"$2"
 	exit 0
     else
-        echo "ERROR: batch file $2 not found. Available batch files are:"
+        echo "ERROR: batch file '$2' not found. Available batch files are:"
         find ${STANDALONE} -name "*.m" -printf "%f\n"
         exit 1
     fi
 fi
 
 # Run CAT
-
 NOW=$(date +%s)
-exec /code/cat_standalone.sh "$@" 2>&1 |tee cat_$NOW.log
+exec ${STANDALONE}/cat_standalone.sh "$@" 2>&1 | tee cat_$NOW.log

makefile

@@ -0,0 +1,5 @@
+tests/data/MoAEpilot:
+	mkdir -p tests/data
+	curl -fL -o moae.zip https://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip
+	unzip -q moae.zip -d tests/data
+	rm -f moae.zip